Collaborative Research: RUI: Structure-Function Relationships and Efficiency of Bacterial Flagellar Motors Using Computational Fluid Dynamics and Directed Evolution Experiments

合作研究：RUI：利用计算流体动力学和定向进化实验研究细菌鞭毛马达的结构功能关系和效率

• 批准号: 2210609
• 负责人: Orrin Shindell
• 金额: $ 54万
• 依托单位: Trinity University
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-09-01 至 2025-08-31
• 项目状态: 未结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2210609&HistoricalAwards=false
• 关键词: Collaborative; Research; RUI; Structure; Function

Bacteria are among the oldest organisms on Earth. Through biological evolution, many bacteria have acquired a biomechanical flagellum consisting of a helical appendage that is rotated by a molecular motor to move them through their fluid environment. Flagellar genetic organization, regulation, and structure are broadly conserved across bacterial species, and flagella play vital roles in the bacterial life cycle, including in host-microbe interactions. Thus, understanding bacterial motility has broad implications in medicine, in biology, and in the development of micro-robotic swimmers. This research aims to understand how the energy efficiency of the bacterial motor has influenced the evolutionary development of the bacterial motility system. The project will create precisely calibrated computational tools to study variants of the medically important organism Pseudomonas aeruginosa with different motor properties. The energy efficiency of each variant will be measured and associated with structural changes in motor components. The computational tools and a library of these motor variants will be made publicly available so that other researchers may use them for related research. The experiments and computations required for this work will all be conducted in tandem with undergraduate students, with the goal that many of them, including students from underrepresented backgrounds, will pursue careers in interdisciplinary scientific research.Recent work has uncovered the molecular structure of the stator unit responsible for generating torque in the bacterial flagellar motor. This project aims to characterize the relationships between specific structural properties of the bacterial stator and its energy efficiency. Strains of P. aeruginosa with suboptimal stators will be created and used in directed evolution experiments to select for variant strains with improved motility. Quantitative microscopy will be used to measure bacterial motion as they move through different fluid environments. Experimentally determined trajectories will be input into precisely calibrated computational fluid dynamics simulations to determine the energy efficiency of the stator. The determination of sequence and structural features of evolved stators with different energy efficiencies will provide insights into the relationship between the mechanical properties and biomolecular structures of nanomotors. Additionally, to study how the presence of a nearby boundary affects the swimming efficiency of the evolved strains, motility experiments will be performed near smooth surfaces and surfaces with tunable viscosity and electrostatic properties. The surfaces will be constructed from lipids and proteins to mimic the environments that P. aeruginosa commonly encounters in its natural environment as it undergoes motile-to-sessile transitions. The calibration measurements will allow other researchers to create additional precisely calibrated computational fluid dynamics models and develop similar computational probes as used in this project. The publicly available library of evolved motor variants and the structure-function map for the stator will deepen the understanding of the relationship between motor proteins and motor performance.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

细菌是地球上最古老的生物之一。通过生物学进化，许多细菌获得了一个由螺旋附件组成的生物力学鞭毛，该螺旋围位由分子运动旋转以使其穿过其液体环境。鞭毛遗传组织，调节和结构在细菌种类中广泛保守，鞭毛在细菌生命周期中起着至关重要的作用，包括在宿主 - 微生物相互作用中。因此，了解细菌运动在医学，生物学和微生物游泳者的发展方面具有广泛的影响。这项研究旨在了解细菌运动的能源效率如何影响细菌运动系统的进化发展。该项目将创建精确校准的计算工具，以研究具有不同运动性能的医学重要生物假单胞菌的变体。将测量每个变体的能源效率，并与运动组件的结构变化相关联。这些电机变体的计算工具和库将公开使用，以便其他研究人员可以将其用于相关研究。这项工作所需的实验和计算将与本科生一起进行，其目标是，其中许多人，包括来自代表性不足的背景的学生，将从事跨学科科学研究的职业。该项目旨在表征细菌定子的特定结构特性与其能源效率之间的关系。铜绿假单胞菌的菌株将在定向的演化实验中创建并使用次优指定，以选择具有改善运动性的变异菌株。定量显微镜将用于测量细菌运动在不同的流体环境中移动。实验确定的轨迹将被输入精确校准的计算流体动力学模拟中，以确定定子的能源效率。确定具有不同能量效率的演变定位的序列和结构特征将为纳米运动的机械性能与生物分子结构之间的关系提供见解。此外，为了研究附近边界的存在如何影响进化菌株的游泳效率，将在具有可调粘度和静电性能的光滑表面和表面附近进行运动实验。表面将从脂质和蛋白质构造，以模仿铜绿假单胞菌通常在自然环境中经历运动到塞维尔过渡时通常遇到的环境。校准测量结果将使其他研究人员能够创建其他精确校准的计算流体动力学模型，并开发与该项目中使用的相似计算探针。公开可用的发展运动变体库和定子的结构功能图将加深对运动蛋白与运动性能之间关系的理解。该奖项反映了NSF的法定任务，并被认为是值得通过基金会的知识分子优点和更广泛影响的评估标准通过评估来进行评估的。